Starting phenix.real_space_refine (version: dev) on Mon Dec 12 17:01:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0x_0583/12_2022/6o0x_0583.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0x_0583/12_2022/6o0x_0583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0x_0583/12_2022/6o0x_0583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0x_0583/12_2022/6o0x_0583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0x_0583/12_2022/6o0x_0583.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0x_0583/12_2022/6o0x_0583.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A ASP 94": "OD1" <-> "OD2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ASP 435": "OD1" <-> "OD2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 967": "NH1" <-> "NH2" Residue "A ARG 1084": "NH1" <-> "NH2" Residue "A ASP 1117": "OD1" <-> "OD2" Residue "A ASP 1135": "OD1" <-> "OD2" Residue "A ARG 1210": "NH1" <-> "NH2" Residue "A ARG 1279": "NH1" <-> "NH2" Residue "A PHE 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1332": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 11257 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8098 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 1112, 8098 Classifications: {'peptide': 1112} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'PTRANS': 29, 'TRANS': 1082} Chain breaks: 5 Unresolved non-hydrogen bonds: 1001 Unresolved non-hydrogen angles: 1217 Unresolved non-hydrogen dihedrals: 802 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 19, 'ASP:plan': 40, 'PHE:plan': 5, 'GLU:plan': 62, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 568 Chain: "B" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2104 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 53, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain breaks: 1 Chain: "c" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 463 Classifications: {'DNA': 23} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 22} Time building chain proxies: 7.45, per 1000 atoms: 0.66 Number of scatterers: 11257 At special positions: 0 Unit cell: (139.612, 127.072, 89.452, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 149 15.00 O 2419 8.00 N 2005 7.00 C 6671 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.37 Conformation dependent library (CDL) restraints added in 1.6 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 52.2% alpha, 6.6% beta 54 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 3.928A pdb=" N LEU A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.977A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.665A pdb=" N GLN A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 271 through 281 removed outlier: 4.161A pdb=" N ALA A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 302 removed outlier: 3.626A pdb=" N PHE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.691A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.587A pdb=" N ILE A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.681A pdb=" N PHE A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.580A pdb=" N VAL A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.260A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.342A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.702A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.537A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.505A pdb=" N SER A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 569 removed outlier: 3.667A pdb=" N TYR A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 626 removed outlier: 4.362A pdb=" N ILE A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 removed outlier: 3.874A pdb=" N LYS A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 703 through 710 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 750 removed outlier: 3.554A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 removed outlier: 3.511A pdb=" N VAL A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.861A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1000 Processing helix chain 'A' and resid 1079 through 1087 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.646A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 3.663A pdb=" N GLY A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1312 removed outlier: 3.797A pdb=" N LEU A1312 " --> pdb=" O ASN A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1316 Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.721A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.475A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 530 Processing sheet with id=AA5, first strand: chain 'A' and resid 1157 through 1167 removed outlier: 3.517A pdb=" N VAL A1145 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A1164 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1324 through 1325 387 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 274 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 97 stacking parallelities Total time for adding SS restraints: 6.20 Time building geometry restraints manager: 5.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1993 1.33 - 1.45: 3596 1.45 - 1.57: 5877 1.57 - 1.69: 294 1.69 - 1.81: 25 Bond restraints: 11785 Sorted by residual: bond pdb=" CD LYS A1334 " pdb=" CE LYS A1334 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.72e+00 bond pdb=" C3' A B 8 " pdb=" O3' A B 8 " ideal model delta sigma weight residual 1.417 1.437 -0.020 1.50e-02 4.44e+03 1.69e+00 bond pdb=" C1' DC c 20 " pdb=" N1 DC c 20 " ideal model delta sigma weight residual 1.490 1.526 -0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" CB LYS A1334 " pdb=" CG LYS A1334 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.33e+00 bond pdb=" CE LYS A1334 " pdb=" NZ LYS A1334 " ideal model delta sigma weight residual 1.489 1.456 0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 11780 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.24: 984 106.24 - 113.16: 6563 113.16 - 120.08: 4269 120.08 - 126.99: 4463 126.99 - 133.91: 415 Bond angle restraints: 16694 Sorted by residual: angle pdb=" CA LYS A1334 " pdb=" CB LYS A1334 " pdb=" CG LYS A1334 " ideal model delta sigma weight residual 114.10 127.36 -13.26 2.00e+00 2.50e-01 4.39e+01 angle pdb=" CB LYS A1334 " pdb=" CG LYS A1334 " pdb=" CD LYS A1334 " ideal model delta sigma weight residual 111.30 123.42 -12.12 2.30e+00 1.89e-01 2.78e+01 angle pdb=" C LYS A1334 " pdb=" CA LYS A1334 " pdb=" CB LYS A1334 " ideal model delta sigma weight residual 109.72 117.55 -7.83 1.73e+00 3.34e-01 2.05e+01 angle pdb=" C3' A B 8 " pdb=" O3' A B 8 " pdb=" P A B 9 " ideal model delta sigma weight residual 120.20 126.08 -5.88 1.50e+00 4.44e-01 1.54e+01 angle pdb=" C GLN A 330 " pdb=" N ASP A 331 " pdb=" CA ASP A 331 " ideal model delta sigma weight residual 121.14 114.28 6.86 1.75e+00 3.27e-01 1.54e+01 ... (remaining 16689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6335 35.97 - 71.95: 262 71.95 - 107.92: 5 107.92 - 143.89: 0 143.89 - 179.86: 3 Dihedral angle restraints: 6605 sinusoidal: 3333 harmonic: 3272 Sorted by residual: dihedral pdb=" CA GLU A 584 " pdb=" C GLU A 584 " pdb=" N ASP A 585 " pdb=" CA ASP A 585 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C4' A B 42 " pdb=" C3' A B 42 " pdb=" O3' A B 42 " pdb=" P G B 43 " ideal model delta sinusoidal sigma weight residual 220.00 40.14 179.86 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' A B 38 " pdb=" C3' A B 38 " pdb=" O3' A B 38 " pdb=" P G B 39 " ideal model delta sinusoidal sigma weight residual 220.00 43.05 176.95 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 6602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1689 0.057 - 0.114: 288 0.114 - 0.171: 42 0.171 - 0.228: 5 0.228 - 0.285: 1 Chirality restraints: 2025 Sorted by residual: chirality pdb=" C3' A B 8 " pdb=" C4' A B 8 " pdb=" O3' A B 8 " pdb=" C2' A B 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C3' A B 38 " pdb=" C4' A B 38 " pdb=" O3' A B 38 " pdb=" C2' A B 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.25 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE A 48 " pdb=" CA ILE A 48 " pdb=" CG1 ILE A 48 " pdb=" CG2 ILE A 48 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 2022 not shown) Planarity restraints: 1579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 74 " 0.049 2.00e-02 2.50e+03 2.28e-02 1.42e+01 pdb=" N9 A B 74 " -0.055 2.00e-02 2.50e+03 pdb=" C8 A B 74 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 74 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A B 74 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 74 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A B 74 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A B 74 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A B 74 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 74 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A B 74 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 75 " 0.032 2.00e-02 2.50e+03 1.39e-02 5.35e+00 pdb=" N9 A B 75 " -0.029 2.00e-02 2.50e+03 pdb=" C8 A B 75 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 75 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A B 75 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A B 75 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 75 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A B 75 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 75 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A B 75 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A B 75 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1300 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO A1301 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A1301 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1301 " 0.031 5.00e-02 4.00e+02 ... (remaining 1576 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3547 2.83 - 3.35: 9228 3.35 - 3.87: 19481 3.87 - 4.38: 20986 4.38 - 4.90: 33652 Nonbonded interactions: 86894 Sorted by model distance: nonbonded pdb=" OG1 THR A 404 " pdb=" OD1 ASP A 406 " model vdw 2.317 2.440 nonbonded pdb=" O ILE A 300 " pdb=" OG SER A 303 " model vdw 2.349 2.440 nonbonded pdb=" O ASP A 483 " pdb=" OG SER A 487 " model vdw 2.356 2.440 nonbonded pdb=" O2' A B 75 " pdb=" O4' A B 76 " model vdw 2.361 2.440 nonbonded pdb=" OG SER A1351 " pdb=" N ILE A1352 " model vdw 2.364 2.520 ... (remaining 86889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 149 5.49 5 S 13 5.16 5 C 6671 2.51 5 N 2005 2.21 5 O 2419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.600 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.100 Process input model: 38.960 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 11785 Z= 0.341 Angle : 0.737 13.257 16694 Z= 0.402 Chirality : 0.045 0.285 2025 Planarity : 0.005 0.057 1579 Dihedral : 16.666 179.863 4481 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.19), residues: 1100 helix: -2.49 (0.16), residues: 526 sheet: -2.08 (0.46), residues: 94 loop : -2.97 (0.22), residues: 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 1.102 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.2086 time to fit residues: 17.9142 Evaluate side-chains 38 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.287 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 6.9990 chunk 93 optimal weight: 0.0980 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 63 optimal weight: 0.0050 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 overall best weight: 2.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 37 ASN A 113 HIS A 187 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN A 402 GLN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 11785 Z= 0.268 Angle : 0.536 5.688 16694 Z= 0.294 Chirality : 0.037 0.149 2025 Planarity : 0.004 0.049 1579 Dihedral : 16.752 177.138 2877 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.23), residues: 1100 helix: -0.44 (0.21), residues: 533 sheet: -1.77 (0.51), residues: 87 loop : -2.54 (0.25), residues: 480 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 1.106 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 50 average time/residue: 0.1633 time to fit residues: 14.2588 Evaluate side-chains 42 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1019 time to fit residues: 2.5558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 11785 Z= 0.330 Angle : 0.561 5.734 16694 Z= 0.303 Chirality : 0.038 0.146 2025 Planarity : 0.004 0.047 1579 Dihedral : 16.890 176.865 2877 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.25), residues: 1100 helix: 0.33 (0.23), residues: 533 sheet: -1.53 (0.53), residues: 87 loop : -2.31 (0.27), residues: 480 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 1.287 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 49 average time/residue: 0.1651 time to fit residues: 14.1769 Evaluate side-chains 42 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1171 time to fit residues: 2.6964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 11785 Z= 0.142 Angle : 0.453 5.745 16694 Z= 0.250 Chirality : 0.034 0.145 2025 Planarity : 0.003 0.042 1579 Dihedral : 16.648 174.552 2877 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.26), residues: 1100 helix: 0.76 (0.23), residues: 537 sheet: -1.38 (0.54), residues: 89 loop : -2.18 (0.27), residues: 474 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 1.074 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 58 average time/residue: 0.1597 time to fit residues: 16.2217 Evaluate side-chains 50 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1100 time to fit residues: 2.8366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.063 11785 Z= 0.625 Angle : 0.747 7.509 16694 Z= 0.392 Chirality : 0.046 0.172 2025 Planarity : 0.004 0.045 1579 Dihedral : 17.272 179.506 2877 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.25), residues: 1100 helix: 0.56 (0.23), residues: 533 sheet: -1.58 (0.51), residues: 91 loop : -2.26 (0.27), residues: 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 34 time to evaluate : 1.136 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 51 average time/residue: 0.1818 time to fit residues: 15.7356 Evaluate side-chains 45 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1049 time to fit residues: 3.8422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN A1241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11785 Z= 0.199 Angle : 0.498 6.282 16694 Z= 0.271 Chirality : 0.036 0.154 2025 Planarity : 0.003 0.045 1579 Dihedral : 16.850 174.222 2877 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.26), residues: 1100 helix: 0.95 (0.24), residues: 534 sheet: -1.11 (0.55), residues: 84 loop : -2.03 (0.27), residues: 482 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 1.174 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 0.1701 time to fit residues: 13.0427 Evaluate side-chains 41 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1171 time to fit residues: 2.0413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 11785 Z= 0.276 Angle : 0.529 6.572 16694 Z= 0.286 Chirality : 0.037 0.144 2025 Planarity : 0.003 0.042 1579 Dihedral : 16.910 174.677 2877 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.26), residues: 1100 helix: 1.03 (0.24), residues: 534 sheet: -1.02 (0.55), residues: 84 loop : -1.99 (0.27), residues: 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 1.140 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 44 average time/residue: 0.1696 time to fit residues: 13.2453 Evaluate side-chains 40 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2981 time to fit residues: 2.6154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 93 optimal weight: 0.0670 chunk 108 optimal weight: 7.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 11785 Z= 0.156 Angle : 0.466 5.736 16694 Z= 0.254 Chirality : 0.035 0.151 2025 Planarity : 0.003 0.040 1579 Dihedral : 16.727 172.364 2877 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.26), residues: 1100 helix: 1.31 (0.24), residues: 531 sheet: -0.80 (0.57), residues: 84 loop : -1.87 (0.28), residues: 485 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 1.043 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.1564 time to fit residues: 12.9757 Evaluate side-chains 43 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1143 time to fit residues: 1.4706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 11785 Z= 0.264 Angle : 0.521 7.069 16694 Z= 0.280 Chirality : 0.037 0.153 2025 Planarity : 0.003 0.040 1579 Dihedral : 16.823 172.324 2877 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.26), residues: 1100 helix: 1.28 (0.24), residues: 533 sheet: -0.80 (0.56), residues: 89 loop : -1.91 (0.28), residues: 478 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 1.159 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 47 average time/residue: 0.1895 time to fit residues: 15.7821 Evaluate side-chains 44 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1030 time to fit residues: 1.9481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11785 Z= 0.210 Angle : 0.502 7.896 16694 Z= 0.269 Chirality : 0.037 0.257 2025 Planarity : 0.003 0.039 1579 Dihedral : 16.767 171.538 2877 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.26), residues: 1100 helix: 1.30 (0.24), residues: 534 sheet: -0.73 (0.56), residues: 89 loop : -1.82 (0.28), residues: 477 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 1.007 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.1579 time to fit residues: 13.3520 Evaluate side-chains 48 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1316 time to fit residues: 1.4934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.077855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.056085 restraints weight = 34804.252| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.73 r_work: 0.2729 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 11785 Z= 0.246 Angle : 0.525 10.143 16694 Z= 0.279 Chirality : 0.038 0.249 2025 Planarity : 0.003 0.039 1579 Dihedral : 16.796 171.972 2877 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1100 helix: 1.32 (0.24), residues: 532 sheet: -0.73 (0.55), residues: 89 loop : -1.82 (0.28), residues: 479 =============================================================================== Job complete usr+sys time: 1791.28 seconds wall clock time: 33 minutes 36.85 seconds (2016.85 seconds total)